Structural and Computational Characterization of a Bridging Zwitterionic-Amidoxime Uranyl Complex.
Ontology highlight
ABSTRACT:
SUBMITTER: Decato DA
PROVIDER: S-EPMC6510399 | biostudies-literature | 2019 Apr
REPOSITORIES: biostudies-literature
Publications
Structural and Computational Characterization of a Bridging Zwitterionic-Amidoxime Uranyl Complex.
Decato Daniel A DA Berryman Orion B OB
Organic chemistry frontiers : an international journal of organic chemistry 20190312 7
A bridging (μ<sub>2</sub>) neutral zwitterionic amidoxime binding mode previously unobserved between amidoximes and uranyl is reported and compared to other uranyl amidoxime complexes. Density functional theory computations show the dinuclear complex exhibits a shallow potential energy surface allowing for facile inclusion of a nonbonding water molecule in the solid-state. ...[more]
Similar Datasets
Project description:The full crystal structure of the copper-uranyl tetrahydroxide mineral (vandenbrandeite), including the positions of the hydrogen atoms, is established by the first time from X-ray diffraction data taken from a natural crystal sample from the Musonoi Mine, Katanga Province, Democratic Republic of Congo. The structure is verified using first-principles solid-state methods. From the optimized structure, the mechanical and dynamical stability of vandenbrandeite is studied and a rich set of mechanical properties are determined. The Raman spectrum is recorded from the natural sample and determined theoretically. Since both spectra have a high-degree of consistence, all spectral bands are rigorously assigned using a theoretical normal-coordinate analysis. Two bands in the Raman spectra, located at 2327 and 1604 cm-1, are recognized as overtones and a band at 1554 cm-1 is identified as a combination band. The fundamental thermodynamic functions of vandenbrandeite are computed as a function of temperature using phonon calculations. These properties, unknown so far, are key-parameters for the performance-assessment of geological repositories for storage of radioactive nuclear waste and for understanding the paragenetic sequence of minerals arising from the corrosion of uranium deposits. The thermodynamic functions are used here to determine the thermodynamic properties of formation of vandenbrandeite in terms of the elements and the Gibbs free-energies and reaction constants for a series of reactions involving vandenbrandeite and a representative subset of the most important secondary phases of spent nuclear fuel. Finally, from the thermodynamic data of these reactions, the relative stability of vandenbrandeite with respect to these phases as a function of temperature and in the presence of hydrogen peroxide is evaluated. Vandenbrandeite is shown to be highly stable under the simultaneous presence of water and hydrogen peroxide.
| S-EPMC9076244 | biostudies-literature
Project description:The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO22+). Although uranyl-protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl-protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl-protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.
| S-EPMC7175365 | biostudies-literature
Project description:Nuclear power facilities are being expanded to satisfy expanding worldwide energy demand. Thus, uranium recovery from secondary resources has become a hot topic in terms of environmental protection and nuclear fuel conservation. Herein, a mesoporous biosorbent of a hybrid magnetic-chitosan nanocomposite functionalized with cysteine (Cys) was synthesized via subsequent heterogeneous nucleation for selectively enhanced uranyl ion (UO22+) sorption. Various analytical tools were used to confirm the mesoporous nanocomposite structural characteristics and confirm the synthetic route. The characteristics of the synthesized nanocomposite were as follows: superparamagnetic with saturation magnetization (MS: 25.81 emu/g), a specific surface area (SBET: 42.56 m2/g) with a unipore mesoporous structure, an amine content of ~2.43 mmol N/g, and a density of ~17.19/nm2. The experimental results showed that the sorption was highly efficient: for the isotherm fitted by the Langmuir equation, the maximum capacity was about 0.575 mmol U/g at pH range 3.5-5.0, and Temperature (25 ± 1 °C); further, there was excellent selectivity for UO22+, likely due to the chemical valent difference. The sorption process was fast (~50 min), simulated with the pseudo-second-order equation, and the sorption half-time (t1/2) was 3.86 min. The sophisticated spectroscopic studies (FTIR and XPS) revealed that the sorption mechanism was linked to complexation and ion exchange by interaction with S/N/O multiple functional groups. The sorption was exothermic, spontaneous, and governed by entropy change. Desorption and regeneration were carried out using an acidified urea solution (0.25 M) that was recycled for a minimum of six cycles, resulting in a sorption and desorption efficiency of over 91%. The as-synthesized nanocomposite's high stability, durability, and chemical resistivity were confirmed over multiple cycles using FTIR and leachability. Finally, the sorbent was efficiently tested for selective uranium sorption from multicomponent acidic simulated nuclear solution. Owing to such excellent performance, the Cys nanocomposite is greatly promising in the uranium recovery field.
| S-EPMC9268972 | biostudies-literature
Project description:The first actinide complexes of the pyridine dipyrrolide (PDP) ligand class, (MesPDPPh)UO2(THF) and (Cl2PhPDPPh)UO2(THF), are reported as the UVI uranyl adducts of the bulky aryl substituted pincers (MesPDPPh)2- and (Cl2PhPDPPh)2- (derived from 2,6-bis(5-(2,4,6-trimethylphenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine (H2MesPDPPh, Mes = 2,4,6-trimethylphenyl), and 2,6-bis(5-(2,6-dichlorophenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine (H2Cl2PhPDPPh, Cl2Ph = 2,6-dichlorophenyl), respectively). Following the in situ deprotonation of the proligand with lithium hexamethyldisilazide to generate the corresponding dilithium salts (e.g., Li2ArPDPPh, Ar = Mes of Cl2Ph), salt metathesis with [UO2Cl2(THF)2]2 afforded both compounds in moderate yields. The characterization of each species has been undertaken by a combination of solid- and solution-state methods, including combustion analysis, infrared, electronic absorption, and NMR spectroscopies. In both complexes, single-crystal X-ray diffraction has revealed a distorted octahedral geometry in the solid state, enforced by the bite angle of the rigid meridional (ArPDPPh)2- pincer ligand. The electrochemical analysis of both compounds by cyclic voltammetry in tetrahydrofuran (THF) reveals rich redox profiles, including events assigned as UVI/UV redox couples. A time-dependent density functional theory study has been performed on (MesPDPPh)UO2(THF) and provides insight into the nature of the transitions that comprise its electronic absorption spectrum.
| S-EPMC9044449 | biostudies-literature
Project description:A diiron complex containing a bridging hydride and a protonated terminal thiolate of the form [(μ,κ2-bdtH)(μ-PPh2)(μ-H)Fe2(CO)5]+ has been investigated through 57Fe nuclear resonance vibrational spectroscopy (NRVS) and interpreted using density functional theory (DFT) calculations. We report the Fe-μH-Fe wagging mode, and indications for Fe-μD stretching vibrations in the D-isotopologue, observed by 57Fe-NRVS. Our combined approach demonstrates an asymmetric sharing of the hydride between the two iron sites that yields two nondegenerate Fe-μH/D stretching vibrations. The studied complex provides an important model relevant to biological hydrogen catalysis intermediates. The complex mimics proposals for the binuclear metal sites in [FeFe] and [NiFe] hydrogenases. It is also an appealing prototype for the 'Janus intermediate' of nitrogenase, which has been proposed to contain two bridging Fe-H-Fe hydrides and two protonated sulfurs at the FeMo-cofactor. The significance of observing indirect effects of the bridging hydride, as well as obstacles in its direct observation, is discussed in the context of biological hydrogen intermediates.
| S-EPMC8159291 | biostudies-literature
Project description:The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrPC, could lead to pathogenic transformation of the latter to the aggregation-prone PrPSc form. Here, the molecular basis of the interactions in the GroEL-PrP complex is studied with cryo-EM and molecular dynamics approaches. The obtained cryo-EM structure shows PrP to be bound to several subunits of GroEL at the level of their apical domains. According to MD simulations, the disordered N-domain of PrP forms much more intermolecular contacts with GroEL. Upon binding to the GroEL, the N-domain of PrP begins to form short helices, while the C-domain of PrP exhibits a tendency to unfold its α2-helix. In the absence of the nucleotides in the system, these processes are manifested at the hundred nanoseconds to microsecond timescale.
| S-EPMC8615626 | biostudies-literature
Project description:A novel uranyl salen-bis-porphyrin complex, in which two porphyrin subunits and salen moiety were directly linked, was synthesized for the recognition of tetrabutylammonium (TBA) amino acids. This uranyl salen complex, due to the presence of porphyrins with their fluorescence properties, represents the first example of a luminescence of uranyl salen complexes. UV/Vis measurements indicate the formation of 1:1 host-guest complexes, whereas UV-vis and fluorescence studies revealed that this complex acts as a receptor for the enantiomeric recognition of ?-aminoacids derivatives, with high association constants and an excellent enantiomeric discrimination between the two enantiomers of phenylalanine-TBA.
| S-EPMC6902086 | biostudies-literature
Project description:A novel water-soluble uranyl-salophen (salophen=N,N'-disalicylidene-o-phenylenediaminate) complex was obtained. Solubility was achieved in aqueous methyl-β-cyclodextrin solutions, taking advantage of the host-guest interactions established with the adamantyl moieties present on the ligand skeleton. Such an approach facilitates the synthesis of the receptor and the purification processes and, in perspective, can be definitely applicable to other molecular scaffolds. UV/Vis titration experiments demonstrate that the capacity of the uranyl-salophen core to behave as a receptor for anions is retained in water and appears comparable with that previously reported for other water-soluble uranyl-salophen systems. Hence the presence of cyclodextrins does not interfere with molecular recognition processes.
| S-EPMC8385332 | biostudies-literature
Project description:Three new uranyl complexes [(UO2)(OAc)2(CMZ)], [(UO2)(OAc)2(MP)] and [(UO2)(OAc)2(SCZ)] were synthesized and characterized by elemental analysis, FT-IR, UV-Vis spectroscopy, powder XRD analysis, and molar conductivity. The IR analysis confirmed binding to the metal ion by the sulfur and ethoxy oxygen atoms in the carbimazole (CMZ) ligand, while in the 6-mercaptopurine (MP) ligand, the sulfur and the N7 nitrogen atom of a purine coordinated binding to the metal ion. The third ligand showed a 1:1 molar ratio and bound via sulfonamide oxygen and the nitrogen of the pyrimidine ring. Analysis of the synthesized complexes also showed that acetate groups had monodentate binding to the (UO22+). Density Functional Theory (DFT) calculations at the B3LYP level showed similar structures to the experimental results. Theoretical quantum parameters predicted the reactivity of the complexes in the order, [(UO2)(OAc)2(SCZ)] > [(UO2)(OAc)2(MP)]> [(UO2)(OAc)2(CMZ)]. DNA binding studies revealed that [(UO2)(OAc)2(SCZ)] and [(UO2)(OAc)2(CMZ)] have the highest binding constant (Kb) among the uranyl complexes. Additionally, strong binding of the MP and CMZ metal complexes to human serum albumin (HSA) were observed by both absorbance and fluorescence approaches. The antibacterial activity of the complexes was also evaluated against four bacterial strains: two gram-negative; Escherichia coli and Klebsiella pneumonia, and two gram-positive; Staphylococcus aureus and Streptococcus mutans. [(UO2)(OAc)2(MP)] had the greatest antibacterial activity against Klebsiella pneumonia, the gram-positive bacteria, with even higher activity than the standard antibiotic. In vitro cytotoxicity tests were also performed against three human cancer lines, and revealed the most cytotoxic complexes to be [(UO2)(OAc)2(SCZ)], which showed moderate activity against a colon cancer cell line. Thus, uranyl addition enhances the antibacterial and anticancer properties of the free ligands.
| S-EPMC8376047 | biostudies-literature
Project description:The FeMoco of nitrogenase is an iron-sulfur cluster with exceptional bond-reducing abilities. ENDOR studies have suggested that E4, the state that binds and reduces N2, contains bridging hydrides as part of the active-site iron-sulfide cluster. However, there are no examples of any isolable iron-sulfide cluster with a hydride, which would test the feasibility of such a species. Here, we describe a diiron sulfide hydride complex that is prepared using a mild method involving C-S cleavage of added thiolate. Its reactions with nitrogenase substrates show that the hydride can act as a base or nucleophile and that reduction can cause the iron atoms to bind N2. These results add experimental support to hydride-based pathways for nitrogenase.
| S-EPMC4818001 | biostudies-literature